I was able to partially solve this by running a small command to source all
my env.sh files before I run all the tests. For example:
export GALAXY_TOOL_DEPENDENCY_DIR=/path/to/tool-dependencies
for i in `find $GALAXY_TOOL_DEPENDENCY_DIR -iname 'env.sh'`; do source $i;
done
sh run_functional_tests.sh -installed
Not sure if it's the best way to handle things, but it works for now.
Aaron
On Fri, Jul 11, 2014 at 2:54 PM, Aaron Petkau aaron.pet...@gmail.com
wrote:
Hello everyone,
I've been trying to get some functional tests developed for my tools and
I'm trying to figure out how to properly run them. I'm following the guide
at https://wiki.galaxyproject.org/TestingInstalledTools but when I run
the functional tests against tools installed from my tool shed I get some
strange error messages like:
Can't open perl script //find-repeats.pl: No such file or directory
It can't find the script because in the tool XML file it is being run
using an environment variable like
command interpreter=perl
/\$VCF2PSEUDO/find-repeats.pl -l $length -p $pid $fasta $out
The environment variable is set up in one of the dependency packages for
this tool.
If I set this environment variable manually export
VCF2PSEUDO=/path/to/dir and then run the tests with:
export GALAXY_TOOL_DEPENDENCY_DIR=tool_dependencies
sh run_functional_tests.sh -installed
Then all my tests properly work.
So, I'm wondering does the run_functional_tests.sh script setup the
environment for dependency packages for each tool? Or is there something
I'm missing?
Thanks and sorry for the longing email. I'm still new to setting up and
using functional tests in Galaxy,
Aaron
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